Objective: to describe relationships between stunting and school performance in children from high social vulnerability populations at Santiago, Chile. Subjects and methods: school performance was compared in three groups of children: group 1 of 85 short stature (height for age (H/A) -1 to -3 SD) children from short parents (-2 SD H/A of standard at age 18 years), group 2 of 76 short children (-2 SD) from not so short parents (-1.99 to 0.5 SD H/A of standard at age 18 years) and group 3 of 86 normal H/A (&plusmn; 0.5 SD) children of not so short parents. Parents literacy, economic resources and family support to learning were also recorded. School performance was assessed by final scores, academic failure, learning disabilities and performance index. Results: short stature children had lower scores in mathematics and spanish, higher risk of learning disabilities and of subject failure. Multivariate model for low performance included to belong to group 2 (OR = 2.48; CI = 1.13 ? 5.46) and low educational level of both parents (OR = 1.52; CI = 1.13 ? 2.03). Adequate performance mode included high literacy of parents (OR = 1.47; CI = 1.16 ? 1.87), families with fewer children under 18 years of age (OR = 2.29; CI = 1.11 ? 4.71), and normal height of the child (OR = 2.18; CI = 1.08 ? 4.39). Conclusion: prevention of secondary stunting may be a good option to reduce low school performance in low socioeconomic level populations